src/jalview/gui/AnnotationColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.bin.Cache;
  24 import jalview.datamodel.AlignmentAnnotation;
  25 import jalview.datamodel.SequenceGroup;
  26 import jalview.schemes.AnnotationColourGradient;
  27 import jalview.schemes.ColourSchemeI;
  28 import jalview.util.MessageManager;
  29
  30 import java.awt.BorderLayout;
  31 import java.awt.Color;
  32 import java.awt.Dimension;
  33 import java.awt.FlowLayout;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.awt.event.MouseAdapter;
  37 import java.awt.event.MouseEvent;
  38 import java.util.Hashtable;
  39 import java.util.Vector;
  40
  41 import javax.swing.BorderFactory;
  42 import javax.swing.JButton;
  43 import javax.swing.JCheckBox;
  44 import javax.swing.JColorChooser;
  45 import javax.swing.JComboBox;
  46 import javax.swing.JInternalFrame;
  47 import javax.swing.JLayeredPane;
  48 import javax.swing.JPanel;
  49 import javax.swing.JSlider;
  50 import javax.swing.JTextField;
  51 import javax.swing.event.ChangeEvent;
  52 import javax.swing.event.ChangeListener;
  53
  54 import net.miginfocom.swing.MigLayout;
  55
  56 public class AnnotationColourChooser extends JPanel
  57 {
  58   JInternalFrame frame;
  59
  60   AlignViewport av;
  61
  62   AlignmentPanel ap;
  63
  64   ColourSchemeI oldcs;
  65
  66   Hashtable oldgroupColours;
  67
  68   jalview.datamodel.AlignmentAnnotation currentAnnotation;
  69
  70   boolean adjusting = false;
  71
  72   /**
  73    * enabled if the user is dragging the slider - try to keep updates to a
  74    * minimun
  75    */
  76   boolean sliderDragging = false;
  77
  78   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  79   {
  80     oldcs = av.getGlobalColourScheme();
  81     if (av.getAlignment().getGroups() != null)
  82     {
  83       oldgroupColours = new Hashtable();
  84       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  85       {
  86         if (sg.cs != null)
  87         {
  88           oldgroupColours.put(sg, sg.cs);
  89         }
  90       }
  91     }
  92     this.av = av;
  93     this.ap = ap;
  94     frame = new JInternalFrame();
  95     frame.setContentPane(this);
  96     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  97     Desktop.addInternalFrame(frame,
  98             MessageManager.getString("label.colour_by_annotation"), 520,
  99             215);
 100
 101     slider.addChangeListener(new ChangeListener()
 102     {
 103       @Override
 104       public void stateChanged(ChangeEvent evt)
 105       {
 106         if (!adjusting)
 107         {
 108           thresholdValue.setText((slider.getValue() / 1000f) + "");
 109           valueChanged(!sliderDragging);
 110         }
 111       }
 112     });
 113     slider.addMouseListener(new MouseAdapter()
 114     {
 115       @Override
 116       public void mousePressed(MouseEvent e)
 117       {
 118         sliderDragging = true;
 119         super.mousePressed(e);
 120       }
 121
 122       @Override
 123       public void mouseDragged(MouseEvent e)
 124       {
 125         sliderDragging = true;
 126         super.mouseDragged(e);
 127       }
 128
 129       @Override
 130       public void mouseReleased(MouseEvent evt)
 131       {
 132         if (sliderDragging)
 133         {
 134           sliderDragging = false;
 135           valueChanged(true);
 136         }
 137         ap.paintAlignment(true);
 138       }
 139     });
 140
 141     if (av.getAlignment().getAlignmentAnnotation() == null)
 142     {
 143       return;
 144     }
 145
 146     // Always get default shading from preferences.
 147     setDefaultMinMax();
 148
 149     adjusting = true;
 150     if (oldcs instanceof AnnotationColourGradient)
 151     {
 152       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 153       currentColours.setSelected(acg.isPredefinedColours()
 154               || acg.getBaseColour() != null);
 155       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 156       {
 157         minColour.setBackground(acg.getMinColour());
 158         maxColour.setBackground(acg.getMaxColour());
 159       }
 160       seqAssociated.setSelected(acg.isSeqAssociated());
 161
 162     }
 163     annotations = new JComboBox(
 164             getAnnotationItems(seqAssociated.isSelected()));
 165
 166     threshold.addItem(MessageManager
 167             .getString("label.threshold_feature_no_thereshold"));
 168     threshold.addItem(MessageManager
 169             .getString("label.threshold_feature_above_thereshold"));
 170     threshold.addItem(MessageManager
 171             .getString("label.threshold_feature_below_thereshold"));
 172
 173     if (oldcs instanceof AnnotationColourGradient)
 174     {
 175       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 176       annotations.setSelectedItem(acg.getAnnotation());
 177       switch (acg.getAboveThreshold())
 178       {
 179       case AnnotationColourGradient.NO_THRESHOLD:
 180         threshold.setSelectedIndex(0);
 181         break;
 182       case AnnotationColourGradient.ABOVE_THRESHOLD:
 183         threshold.setSelectedIndex(1);
 184         break;
 185       case AnnotationColourGradient.BELOW_THRESHOLD:
 186         threshold.setSelectedIndex(2);
 187         break;
 188       default:
 189         throw new Error(
 190                 "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
 191       }
 192       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 193       thresholdValue.setText("" + acg.getAnnotationThreshold());
 194     }
 195
 196     try
 197     {
 198       jbInit();
 199     } catch (Exception ex)
 200     {
 201     }
 202
 203     adjusting = false;
 204
 205     changeColour();
 206     frame.invalidate();
 207     frame.pack();
 208
 209   }
 210
 211   private Vector<String> getAnnotationItems(boolean isSeqAssociated)
 212   {
 213     Vector<String> list = new Vector<String>();
 214     int index = 1;
 215     int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
 216     boolean enableSeqAss = false;
 217     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 218     {
 219       if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
 220       {
 221         if (isSeqAssociated)
 222         {
 223           continue;
 224         }
 225       }
 226       else
 227       {
 228         enableSeqAss = true;
 229       }
 230       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 231       if (!list.contains(label))
 232       {
 233         anmap[list.size()] = i;
 234         list.add(label);
 235
 236       }
 237       else
 238       {
 239         if (!isSeqAssociated)
 240         {
 241           anmap[list.size()] = i;
 242           list.add(label + "_" + (index++));
 243         }
 244       }
 245     }
 246     seqAssociated.setEnabled(enableSeqAss);
 247     this.annmap = new int[list.size()];
 248     System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
 249     return list;
 250   }
 251
 252   private void setDefaultMinMax()
 253   {
 254     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 255             Color.orange));
 256     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 257             Color.red));
 258   }
 259
 260   public AnnotationColourChooser()
 261   {
 262     try
 263     {
 264       jbInit();
 265     } catch (Exception ex)
 266     {
 267       ex.printStackTrace();
 268     }
 269   }
 270
 271   private void jbInit() throws Exception
 272   {
 273     minColour.setFont(JvSwingUtils.getLabelFont());
 274     minColour.setBorder(BorderFactory.createEtchedBorder());
 275     minColour.setPreferredSize(new Dimension(40, 20));
 276     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 277     minColour.addMouseListener(new MouseAdapter()
 278     {
 279       @Override
 280       public void mousePressed(MouseEvent e)
 281       {
 282         if (minColour.isEnabled())
 283         {
 284           minColour_actionPerformed();
 285         }
 286       }
 287     });
 288     maxColour.setFont(JvSwingUtils.getLabelFont());
 289     maxColour.setBorder(BorderFactory.createEtchedBorder());
 290     maxColour.setPreferredSize(new Dimension(40, 20));
 291     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 292     maxColour.addMouseListener(new MouseAdapter()
 293     {
 294       @Override
 295       public void mousePressed(MouseEvent e)
 296       {
 297         if (maxColour.isEnabled())
 298         {
 299           maxColour_actionPerformed();
 300         }
 301       }
 302     });
 303     ok.setOpaque(false);
 304     ok.setText(MessageManager.getString("action.ok"));
 305     ok.addActionListener(new ActionListener()
 306     {
 307       @Override
 308       public void actionPerformed(ActionEvent e)
 309       {
 310         ok_actionPerformed(e);
 311       }
 312     });
 313     cancel.setOpaque(false);
 314     cancel.setText(MessageManager.getString("action.cancel"));
 315     cancel.addActionListener(new ActionListener()
 316     {
 317       @Override
 318       public void actionPerformed(ActionEvent e)
 319       {
 320         cancel_actionPerformed(e);
 321       }
 322     });
 323     defColours.setOpaque(false);
 324     defColours.setText(MessageManager.getString("action.set_defaults"));
 325     defColours.setToolTipText(MessageManager
 326             .getString("label.reset_min_max_colours_to_defaults"));
 327     defColours.addActionListener(new ActionListener()
 328     {
 329
 330       @Override
 331       public void actionPerformed(ActionEvent arg0)
 332       {
 333         resetColours_actionPerformed(arg0);
 334       }
 335     });
 336
 337     annotations.addActionListener(new ActionListener()
 338     {
 339       @Override
 340       public void actionPerformed(ActionEvent e)
 341       {
 342         annotations_actionPerformed(e);
 343       }
 344     });
 345     threshold.addActionListener(new ActionListener()
 346     {
 347       @Override
 348       public void actionPerformed(ActionEvent e)
 349       {
 350         threshold_actionPerformed(e);
 351       }
 352     });
 353     thresholdValue.addActionListener(new ActionListener()
 354     {
 355       @Override
 356       public void actionPerformed(ActionEvent e)
 357       {
 358         thresholdValue_actionPerformed(e);
 359       }
 360     });
 361     slider.setPaintLabels(false);
 362     slider.setPaintTicks(true);
 363     slider.setBackground(Color.white);
 364     slider.setEnabled(false);
 365     slider.setOpaque(false);
 366     slider.setPreferredSize(new Dimension(100, 32));
 367     thresholdValue.setEnabled(false);
 368     thresholdValue.setColumns(7);
 369     currentColours.setFont(JvSwingUtils.getLabelFont());
 370     currentColours.setOpaque(false);
 371     currentColours.setText(MessageManager
 372             .getString("label.use_original_colours"));
 373     currentColours.addActionListener(new ActionListener()
 374     {
 375       @Override
 376       public void actionPerformed(ActionEvent e)
 377       {
 378         currentColours_actionPerformed(e);
 379       }
 380     });
 381     thresholdIsMin.setBackground(Color.white);
 382     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 383     thresholdIsMin.setText(MessageManager
 384             .getString("label.threshold_minmax"));
 385     thresholdIsMin.addActionListener(new ActionListener()
 386     {
 387       @Override
 388       public void actionPerformed(ActionEvent actionEvent)
 389       {
 390         thresholdIsMin_actionPerformed(actionEvent);
 391       }
 392     });
 393     seqAssociated.setBackground(Color.white);
 394     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 395     seqAssociated.setText(MessageManager
 396             .getString("label.per_sequence_only"));
 397     seqAssociated.addActionListener(new ActionListener()
 398     {
 399
 400       @Override
 401       public void actionPerformed(ActionEvent arg0)
 402       {
 403         seqAssociated_actionPerformed(arg0);
 404       }
 405     });
 406
 407     this.setLayout(borderLayout1);
 408     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 409     jPanel1.setBackground(Color.white);
 410     jPanel2.setBackground(Color.white);
 411
 412     jPanel1.add(ok);
 413     jPanel1.add(cancel);
 414     jPanel2.add(annotations, "grow, wrap");
 415     jPanel2.add(seqAssociated);
 416     jPanel2.add(currentColours);
 417     JPanel colpanel = new JPanel(new FlowLayout());
 418     colpanel.setBackground(Color.white);
 419     colpanel.add(minColour);
 420     colpanel.add(maxColour);
 421     jPanel2.add(colpanel, "wrap");
 422     jPanel2.add(threshold);
 423     jPanel2.add(defColours, "skip 1, wrap");
 424     jPanel2.add(thresholdIsMin);
 425     jPanel2.add(slider, "grow");
 426     jPanel2.add(thresholdValue, "grow");
 427     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 428     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 429     this.validate();
 430   }
 431
 432   protected void seqAssociated_actionPerformed(ActionEvent arg0)
 433   {
 434     adjusting = true;
 435     String cursel = (String) annotations.getSelectedItem();
 436     boolean isvalid = false, isseqs = seqAssociated.isSelected();
 437     this.annotations.removeAllItems();
 438     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
 439     {
 440       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
 441       {
 442         isvalid = true;
 443         cursel = anitem;
 444       }
 445       this.annotations.addItem(anitem);
 446     }
 447     adjusting = false;
 448     if (isvalid)
 449     {
 450       this.annotations.setSelectedItem(cursel);
 451     }
 452     else
 453     {
 454       if (annotations.getItemCount() > 0)
 455       {
 456         annotations.setSelectedIndex(0);
 457       }
 458     }
 459   }
 460
 461   protected void resetColours_actionPerformed(ActionEvent arg0)
 462   {
 463     setDefaultMinMax();
 464     changeColour();
 465   }
 466
 467   JComboBox annotations;
 468
 469   int[] annmap;
 470
 471   JPanel minColour = new JPanel();
 472
 473   JPanel maxColour = new JPanel();
 474
 475   JButton defColours = new JButton();
 476
 477   JButton ok = new JButton();
 478
 479   JButton cancel = new JButton();
 480
 481   JPanel jPanel1 = new JPanel();
 482
 483   JPanel jPanel2 = new JPanel();
 484
 485   BorderLayout borderLayout1 = new BorderLayout();
 486
 487   JComboBox threshold = new JComboBox();
 488
 489   JSlider slider = new JSlider();
 490
 491   JTextField thresholdValue = new JTextField(20);
 492
 493   JCheckBox currentColours = new JCheckBox();
 494
 495   JCheckBox thresholdIsMin = new JCheckBox();
 496
 497   JCheckBox seqAssociated = new JCheckBox();
 498
 499   public void minColour_actionPerformed()
 500   {
 501     Color col = JColorChooser.showDialog(this,
 502             "Select Colour for Minimum Value", minColour.getBackground());
 503     if (col != null)
 504     {
 505       minColour.setBackground(col);
 506     }
 507     minColour.repaint();
 508     changeColour();
 509   }
 510
 511   public void maxColour_actionPerformed()
 512   {
 513     Color col = JColorChooser.showDialog(this,
 514             "Select Colour for Maximum Value", maxColour.getBackground());
 515     if (col != null)
 516     {
 517       maxColour.setBackground(col);
 518     }
 519     maxColour.repaint();
 520     changeColour();
 521   }
 522
 523   void changeColour()
 524   {
 525     // Check if combobox is still adjusting
 526     if (adjusting)
 527     {
 528       return;
 529     }
 530
 531     currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 532             .getSelectedIndex()]];
 533
 534     int aboveThreshold = -1;
 535     if (threshold.getSelectedIndex() == 1)
 536     {
 537       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 538     }
 539     else if (threshold.getSelectedIndex() == 2)
 540     {
 541       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 542     }
 543
 544     slider.setEnabled(true);
 545     thresholdValue.setEnabled(true);
 546     thresholdIsMin.setEnabled(true);
 547
 548     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 549     {
 550       slider.setEnabled(false);
 551       thresholdValue.setEnabled(false);
 552       thresholdValue.setText("");
 553       thresholdIsMin.setEnabled(false);
 554     }
 555     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 556             && currentAnnotation.threshold == null)
 557     {
 558       currentAnnotation
 559               .setThreshold(new jalview.datamodel.GraphLine(
 560                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
 561                       "Threshold", Color.black));
 562     }
 563
 564     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 565     {
 566       adjusting = true;
 567       float range = currentAnnotation.graphMax * 1000
 568               - currentAnnotation.graphMin * 1000;
 569
 570       slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
 571       slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
 572       slider.setValue((int) (currentAnnotation.threshold.value * 1000));
 573       thresholdValue.setText(currentAnnotation.threshold.value + "");
 574       slider.setMajorTickSpacing((int) (range / 10f));
 575       slider.setEnabled(true);
 576       thresholdValue.setEnabled(true);
 577       adjusting = false;
 578     }
 579
 580     AnnotationColourGradient acg = null;
 581     if (currentColours.isSelected())
 582     {
 583       acg = new AnnotationColourGradient(currentAnnotation,
 584               av.getGlobalColourScheme(), aboveThreshold);
 585     }
 586     else
 587     {
 588       acg = new AnnotationColourGradient(currentAnnotation,
 589               minColour.getBackground(), maxColour.getBackground(),
 590               aboveThreshold);
 591     }
 592     acg.setSeqAssociated(seqAssociated.isSelected());
 593
 594     if (currentAnnotation.graphMin == 0f
 595             && currentAnnotation.graphMax == 0f)
 596     {
 597       acg.setPredefinedColours(true);
 598     }
 599
 600     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 601
 602     av.setGlobalColourScheme(acg);
 603
 604     if (av.getAlignment().getGroups() != null)
 605     {
 606
 607       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 608       {
 609         if (sg.cs == null)
 610         {
 611           continue;
 612         }
 613
 614         if (currentColours.isSelected())
 615         {
 616           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 617                   aboveThreshold);
 618           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 619                   .isSelected());
 620
 621         }
 622         else
 623         {
 624           sg.cs = new AnnotationColourGradient(currentAnnotation,
 625                   minColour.getBackground(), maxColour.getBackground(),
 626                   aboveThreshold);
 627           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 628                   .isSelected());
 629         }
 630
 631       }
 632     }
 633     ap.alignmentChanged();
 634     // ensure all associated views (overviews, structures, etc) are notified of
 635     // updated colours.
 636     ap.paintAlignment(true);
 637   }
 638
 639   public void ok_actionPerformed(ActionEvent e)
 640   {
 641     changeColour();
 642     try
 643     {
 644       frame.setClosed(true);
 645     } catch (Exception ex)
 646     {
 647     }
 648   }
 649
 650   public void cancel_actionPerformed(ActionEvent e)
 651   {
 652     reset();
 653     // ensure all original colouring is propagated to listeners.
 654     ap.paintAlignment(true);
 655     try
 656     {
 657       frame.setClosed(true);
 658     } catch (Exception ex)
 659     {
 660     }
 661   }
 662
 663   void reset()
 664   {
 665     av.setGlobalColourScheme(oldcs);
 666     if (av.getAlignment().getGroups() != null)
 667     {
 668
 669       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 670       {
 671         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
 672       }
 673     }
 674   }
 675
 676   public void thresholdCheck_actionPerformed(ActionEvent e)
 677   {
 678     changeColour();
 679   }
 680
 681   public void annotations_actionPerformed(ActionEvent e)
 682   {
 683     changeColour();
 684   }
 685
 686   public void threshold_actionPerformed(ActionEvent e)
 687   {
 688     changeColour();
 689   }
 690
 691   public void thresholdValue_actionPerformed(ActionEvent e)
 692   {
 693     try
 694     {
 695       float f = Float.parseFloat(thresholdValue.getText());
 696       slider.setValue((int) (f * 1000));
 697     } catch (NumberFormatException ex)
 698     {
 699     }
 700   }
 701
 702   public void valueChanged(boolean updateAllAnnotation)
 703   {
 704     if (currentColours.isSelected()
 705             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 706     {
 707       changeColour();
 708     }
 709     currentAnnotation.threshold.value = slider.getValue() / 1000f;
 710     propagateSeqAssociatedThreshold(updateAllAnnotation);
 711     ap.paintAlignment(false);
 712   }
 713
 714   private void propagateSeqAssociatedThreshold(boolean allAnnotation)
 715   {
 716     if (currentAnnotation.sequenceRef == null
 717             || currentAnnotation.threshold == null)
 718     {
 719       return;
 720     }
 721     // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation
 722     // is false, since we only need to provide a quick visual indicator
 723
 724     float thr = currentAnnotation.threshold.value;
 725     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 726     {
 727       AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
 728       if (aa.label.equals(currentAnnotation.label))
 729       {
 730         aa.threshold.value = thr;
 731       }
 732     }
 733   }
 734
 735   public void currentColours_actionPerformed(ActionEvent e)
 736   {
 737     if (currentColours.isSelected())
 738     {
 739       reset();
 740     }
 741
 742     maxColour.setEnabled(!currentColours.isSelected());
 743     minColour.setEnabled(!currentColours.isSelected());
 744
 745     changeColour();
 746   }
 747
 748   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 749   {
 750     changeColour();
 751   }
 752
 753 }